8CIX: Beta sliding clamp

DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with Griselimycin. Determined by X-ray diffraction at 1.76 Å resolution. Released 29 Nov 2023.

Method: X-ray diffraction
Resolution: 1.76 Å
Organisms: Escherichia coli, Streptomyces griseus
Chains: 2
Atoms: 3,462
Mol. weight: 42.78 kDa
Ligands: MG, CA
Released: 29 Nov 2023

Explore 8CIX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CIX contains 16 α-helices and 27 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	7-17	11
α-helix	28-31	4
β-strand	32-38	7	2
β-strand	41-47	7	2
β-strand	51-58	8	2
β-strand	64	1	1
β-strand	66-71	6	2
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	1
β-strand	96-101	6	1
β-strand	104-109	6	1
β-strand	111	1	2
α-helix	113-115	3
β-strand	124-130	7	2
α-helix	132-142	11
α-helix	143-145	3
α-helix	153-156	4
β-strand	158-172	15	3
β-strand	176-195	20	3
α-helix	197-206	10
β-strand	214-219	6	2
β-strand	222-227	6	2
β-strand	230-235	6	2
α-helix	236	1
β-strand	237	1	3
α-helix	238	1
α-helix	244-246	3
β-strand	254-259	6	3
α-helix	260-271	12
β-strand	280-286	7	4
β-strand	289-295	7	4
β-strand	301-307	7	4
β-strand	309	1	3
β-strand	315-320	6	4
α-helix	321-330	10
β-strand	335-340	6	3
β-strand	347-351	5	3
β-strand	357-361	5	3
α-helix	362-363	2
β-strand	364	1	4
α-helix	365	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta sliding clamp	A	protein	369	Escherichia coli	P0A988 (AlphaFold model)
Griselimycin	B	protein	11	Streptomyces griseus

Sequence of entity 1 (A), FASTA

>8CIX_1 Beta sliding clamp (chains A)
GGRMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARV
ALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFP
NLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRL
AVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLV
DGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNP
EQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSA
AYVVMPMRL

Sequence of entity 2 (B), FASTA

>8CIX_2 Griselimycin (chains B)
XVPTLPLVPXG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
CA	Calcium ion	Ca	7

Water and common crystallization additives (NA, ACT, GOL) are not listed.

Primary citation

Elucidation of unusual biosynthesis and DnaN-targeting mode of action of potent anti-tuberculosis antibiotics Mycoplanecins. Fu, C., Liu, Y., Walt, C. et al. Nat Commun (2024) 15:791-791. DOI 10.1038/s41467-024-44953-5 · PubMed

Other PDB entries of the same protein (UniProt P0A988 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PAY 1.21 Å, Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 2.
8PAT 1.45 Å, Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 3.
4K3L 1.5 Å, E. coli sliding clamp in complex with AcLF dipeptide
8CIY 1.54 Å, DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with…
7AZ8 1.61 Å, DNA polymerase sliding clamp from Escherichia coli with peptide 43 bound
4MJR 1.62 Å, E. coli sliding clamp in complex with (S)-Carprofen
6FVM 1.63 Å, Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide
3D1G 1.64 Å, Structure of a small molecule inhibitor bound to a DNA sliding clamp
1OK7 1.65 Å, A Conserved protein binding-site on Bacterial Sliding Clamps
7AZ7 1.65 Å, DNA polymerase sliding clamp from Escherichia coli with peptide 37 bound
4N96 1.7 Å, E. coli sliding clamp in complex with 6-nitroindazole
4N98 1.7 Å, E. coli sliding clamp in complex with 4'-fluorobiphenyl-4-carboxylic acid

Browse structure collections

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